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1 #ifndef BWTALN_H
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2 #define BWTALN_H
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3
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4 #include <stdint.h>
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5 #include "bwt.h"
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6
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7 #define BWA_TYPE_NO_MATCH 0
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8 #define BWA_TYPE_UNIQUE 1
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9 #define BWA_TYPE_REPEAT 2
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10 #define BWA_TYPE_MATESW 3
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11
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12 #define SAM_FPD 1 // paired
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13 #define SAM_FPP 2 // properly paired
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14 #define SAM_FSU 4 // self-unmapped
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15 #define SAM_FMU 8 // mate-unmapped
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16 #define SAM_FSR 16 // self on the reverse strand
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17 #define SAM_FMR 32 // mate on the reverse strand
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18 #define SAM_FR1 64 // this is read one
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19 #define SAM_FR2 128 // this is read two
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20 #define SAM_FSC 256 // secondary alignment
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21
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22 #define BWA_AVG_ERR 0.02
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23 #define BWA_MIN_RDLEN 35 // for read trimming
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24
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25 #define BWA_MAX_BCLEN 63 // maximum barcode length; 127 is the maximum
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26
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27 #ifndef bns_pac
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28 #define bns_pac(pac, k) ((pac)[(k)>>2] >> ((~(k)&3)<<1) & 3)
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29 #endif
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30
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31 typedef struct {
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32 bwtint_t w;
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33 int bid;
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34 } bwt_width_t;
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35
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36 typedef struct {
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37 uint32_t n_mm:16, n_gapo:8, n_gape:8;
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38 int score;
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39 bwtint_t k, l;
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40 } bwt_aln1_t;
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41
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42 typedef uint16_t bwa_cigar_t;
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43 /* rgoya: If changing order of bytes, beware of operations like:
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44 * s->cigar[0] += s->full_len - s->len;
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45 */
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46 #define CIGAR_OP_SHIFT 14
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47 #define CIGAR_LN_MASK 0x3fff
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48
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49 #define __cigar_op(__cigar) ((__cigar)>>CIGAR_OP_SHIFT)
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50 #define __cigar_len(__cigar) ((__cigar)&CIGAR_LN_MASK)
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51 #define __cigar_create(__op, __len) ((__op)<<CIGAR_OP_SHIFT | (__len))
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52
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53 typedef struct {
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54 uint32_t n_cigar:15, gap:8, mm:8, strand:1;
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55 bwtint_t pos;
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56 bwa_cigar_t *cigar;
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57 } bwt_multi1_t;
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58
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59 typedef struct {
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60 char *name;
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61 ubyte_t *seq, *rseq, *qual;
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62 uint32_t len:20, strand:1, type:2, dummy:1, extra_flag:8;
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63 uint32_t n_mm:8, n_gapo:8, n_gape:8, mapQ:8;
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64 int score;
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65 int clip_len;
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66 // alignments in SA coordinates
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67 int n_aln;
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68 bwt_aln1_t *aln;
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69 // multiple hits
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70 int n_multi;
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71 bwt_multi1_t *multi;
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72 // alignment information
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73 bwtint_t sa, pos;
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74 uint64_t c1:28, c2:28, seQ:8; // number of top1 and top2 hits; single-end mapQ
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75 int n_cigar;
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76 bwa_cigar_t *cigar;
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77 // for multi-threading only
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78 int tid;
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79 // barcode
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80 char bc[BWA_MAX_BCLEN+1]; // null terminated; up to BWA_MAX_BCLEN bases
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81 // NM and MD tags
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82 uint32_t full_len:20, nm:12;
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83 char *md;
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84 } bwa_seq_t;
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85
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86 #define BWA_MODE_GAPE 0x01
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87 #define BWA_MODE_COMPREAD 0x02
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88 #define BWA_MODE_LOGGAP 0x04
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89 #define BWA_MODE_CFY 0x08
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90 #define BWA_MODE_NONSTOP 0x10
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91 #define BWA_MODE_BAM 0x20
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92 #define BWA_MODE_BAM_SE 0x40
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93 #define BWA_MODE_BAM_READ1 0x80
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94 #define BWA_MODE_BAM_READ2 0x100
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95 #define BWA_MODE_IL13 0x200
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96
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97 typedef struct {
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98 int s_mm, s_gapo, s_gape;
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99 int mode; // bit 24-31 are the barcode length
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100 int indel_end_skip, max_del_occ, max_entries;
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101 float fnr;
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102 int max_diff, max_gapo, max_gape;
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103 int max_seed_diff, seed_len;
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104 int n_threads;
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105 int max_top2;
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106 int trim_qual;
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107 } gap_opt_t;
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108
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109 #define BWA_PET_STD 1
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110 #define BWA_PET_SOLID 2
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111
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112 typedef struct {
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113 int max_isize, force_isize;
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114 int max_occ;
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115 int n_multi, N_multi;
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116 int type, is_sw, is_preload;
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117 double ap_prior;
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118 } pe_opt_t;
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119
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120 struct __bwa_seqio_t;
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121 typedef struct __bwa_seqio_t bwa_seqio_t;
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122
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123 #ifdef __cplusplus
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124 extern "C" {
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125 #endif
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126
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127 gap_opt_t *gap_init_opt();
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128 void bwa_aln_core(const char *prefix, const char *fn_fa, const gap_opt_t *opt);
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129
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130 bwa_seqio_t *bwa_seq_open(const char *fn);
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131 bwa_seqio_t *bwa_bam_open(const char *fn, int which);
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132 void bwa_seq_close(bwa_seqio_t *bs);
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133 void seq_reverse(int len, ubyte_t *seq, int is_comp);
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134 bwa_seq_t *bwa_read_seq(bwa_seqio_t *seq, int n_needed, int *n, int mode, int trim_qual);
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135 void bwa_free_read_seq(int n_seqs, bwa_seq_t *seqs);
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136
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137 int bwa_cal_maxdiff(int l, double err, double thres);
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138 void bwa_cal_sa_reg_gap(int tid, bwt_t *const bwt, int n_seqs, bwa_seq_t *seqs, const gap_opt_t *opt);
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139
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140 void bwa_cs2nt_core(bwa_seq_t *p, bwtint_t l_pac, ubyte_t *pac);
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141
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142
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143 /* rgoya: Temporary clone of aln_path2cigar to accomodate for bwa_cigar_t,
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144 __cigar_op and __cigar_len while keeping stdaln stand alone */
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145 #include "stdaln.h"
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146
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147 bwa_cigar_t *bwa_aln_path2cigar(const path_t *path, int path_len, int *n_cigar);
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148
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149 #ifdef __cplusplus
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150 }
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151 #endif
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152
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153 #endif
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